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- PDB-5k1m: Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) i... -

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Basic information

Entry
Database: PDB / ID: 5k1m
TitleCrystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) in complex with p-methoxyphenol
ComponentsNAD(P)H:flavin oxidoreductase Sye4
KeywordsOXIDOREDUCTASE / COFACTOR-BINDING
Function / homology
Function and homology information


flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / FMN binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-methoxyphenol / FLAVIN MONONUCLEOTIDE / NAD(P)H:flavin oxidoreductase Sye4
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsElegheert, J. / Brige, A. / Savvides, S.N.
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.
Authors: Elegheert, J. / Brige, A. / Van Beeumen, J. / Savvides, S.N.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)H:flavin oxidoreductase Sye4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3308
Polymers39,1291
Non-polymers1,2017
Water8,107450
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.180, 54.830, 103.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD(P)H:flavin oxidoreductase Sye4


Mass: 39129.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: sye4, SO_3392 / Plasmid: PACYC-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EBV3, flavin reductase (NADPH)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-4KS / 4-methoxyphenol


Mass: 124.137 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.97 % / Description: clothes pin
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 1.6 M sodium citrate tribasic dihydrate pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 47629 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.4
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.378

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5N

4b5n


Resolution: 1.5→19.849 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 15.6
RfactorNum. reflection% reflection
Rfree0.1736 1975 4.15 %
Rwork0.1424 --
obs0.1437 47628 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 76 450 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052993
X-RAY DIFFRACTIONf_angle_d1.0534097
X-RAY DIFFRACTIONf_dihedral_angle_d15.6171117
X-RAY DIFFRACTIONf_chiral_restr0.062450
X-RAY DIFFRACTIONf_plane_restr0.006532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.27441320.22673242X-RAY DIFFRACTION99
1.5375-1.57910.24611630.20623211X-RAY DIFFRACTION99
1.5791-1.62550.22681310.19613187X-RAY DIFFRACTION99
1.6255-1.67790.22751330.18483244X-RAY DIFFRACTION99
1.6779-1.73790.22491470.17413213X-RAY DIFFRACTION99
1.7379-1.80740.19931370.16163230X-RAY DIFFRACTION98
1.8074-1.88960.1911290.1473240X-RAY DIFFRACTION98
1.8896-1.98920.17221560.13193180X-RAY DIFFRACTION98
1.9892-2.11370.15711310.1253217X-RAY DIFFRACTION98
2.1137-2.27660.16141190.11873245X-RAY DIFFRACTION97
2.2766-2.50530.16821420.1233234X-RAY DIFFRACTION98
2.5053-2.86690.14371520.12453320X-RAY DIFFRACTION100
2.8669-3.60850.14561440.12543375X-RAY DIFFRACTION100
3.6085-19.85030.1571590.1383515X-RAY DIFFRACTION100

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